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Input:One strand or two strands in 5'-3' orientation of siRNA of known efficiency
Concatenation of both given siRNA strands (or one given strand and one added) with flanking sequences and loop sequence of pri-miRNA (caps) taken from created pri-miRNA database.
Analysis of sh-miRNA structure with mfold program. Comparison with structure of endogenous pri-miRNAs
aggcaagaugcuggcauagcuugcuaugccaacauauugccau
CAUAACAACGAAGAGGGAUGGUAUUGCUCCUGUAACUCGGAACUGGAGAGGaggcaagaugcuggcauagcuGUUGAACUGGGAACCugcuaugccaacauauugccauCUUUCCUGUCUGACAGCAGCUUGGCUACCUCCGUCCUGUUCCUCCUUGUCUU
sh-miR Designer is a so�ware aimed for fast and efficient design of effec�ve RNA interference (RNAi) reagents - sh-miRs, also known as ar�ficial miRNAs. sh-miRs are RNA par�cles whose structure is based on miRNA precursor pri-miRNA, but sequence interac�ng with transcript is changed depending on research purpose. Maintenance of structure of pri-miRNA is very important to enable cellular processing (performed mainly by endonucleases Drosha and Dicer) and therefore ensure func�onality of ar�ficial par�cles. sh-miRs delivered to cells on gene�c vectors - plasmids or viral vectors - enter natural RNAi pathway and silence target mRNA. They can be used in gene�c therapies and basic biomedical research.
pri-miRNAdatabase
Scoring:1.Structure2.Same first nucleotides of siRNA and miRNA sequence3.Endogenous pri-miRNA product homogeneity (isomirs)
Output:2-3 sh-miRs with best scoring results ordered from the best onepdf with 2D structureweb link to miRbase site of pri-miRNA, which flanking sequences where used
'name': name, 'flanks3_s': flanks3_s, 'flanks3_a': flanks3_a, 'flanks5_s': flanks5_s, 'flanks5_a': flanks5_a, 'loop_s': loop_s, 'loop_a': loop_a, 'miRNA_s': miRNA_s, 'miRNA_a': miRNA_a, 'miRNA_length': miRNA_length, 'miRNA_min': miRNA_min, 'miRNA_max': miRNA_max, 'miRNA_end_5': miRNA_end_5, 'miRNA_end_3': miRNA_end_3, 'structure': structure, 'homogeneity': homogeneity, 'miRBase_link': miRBase_link
155 pri-miRNA
AG
G
C
UU
G
C
UG
U
A
G
G
C
U
G
U
A
U
G
C
U
G
U
U
U
G
U
A
U
U
C
A
G
C
C
C
A
U
A
G
C
G
C
U
U
U
U
G
CC U
C
C
A
A
C
UG
G
C
G
C
U
A
U
G
G
C
G
A
A
U
A
C
A
A
A
C
A
G
U
G
U
A
UGA
UG
C
C
U
GU
U
A
CU
A
G
C
A
U
U
C
A
C
A
U
G
GA
A
C
A
AAU
U
GC
U
G
C
C
G
U
G
G
G
A
GGAUGA
CA
A
A
G
A 5’3’
20
40
60
80
100
120
140
AG G
C
UU
G
C
UG
U
A
G
G
C
U
G
U
A
U
G
C
U
G
U
U
A
A
U
G
C
U
A
A
U
C
G
U
G
A
U
A
G
G
G
G
U
U
U
U
G
CC U
C
C
A
AC
UG
A
C
U
C
C
U
A
C
A
U
A
U
U
A
G
C
A
U
U
A
A
C
A
G
U
G
U
A
UGA
UG
C
C
U
G
U
U
A
CU
A
G
C
A
U
U
C
A
C
A
U
G
G
A
A
C
A
AAU
U
GC
U
G
C
C
G
U
G
G
G
A
GGAUG
AC
A
A
A
G
A 5’
3’
20
40
60
80
100
120
140
Drosha cut
sh-miR designer
Dicer cut
tool for construction of RNA interference reagents: sh-miRs
sh-miRNA with siRNA targeted on luciferase transcriptin 155 pri-miRNA flansking sequence